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Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach.

Boulesteix AL, Strimmer K.

Theor Biol Med Model. 2005 Jun 24;2:23.PMID: 15978125 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcriptome network component analysis with limited microarray data.

Galbraith SJ, Tran LM, Liao JC.

Bioinformatics. 2006 Aug 1;22(15):1886-94. Epub 2006 Jun 9.PMID: 16766556 [PubMed - indexed for MEDLINE]Related articlesFree article

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.

Gao F, Foat BC, Bussemaker HJ.

BMC Bioinformatics. 2004 Mar 18;5:31.PMID: 15113405 [PubMed - indexed for MEDLINE]Related articlesFree article

Systematic identification of cell cycle regulated transcription factors from microarray time series data.

Cheng C, Li LM.

BMC Genomics. 2008 Mar 3;9:116.PMID: 18315882 [PubMed - indexed for MEDLINE]Related articlesFree article

A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data.

Thomas R, Paredes CJ, Mehrotra S, Hatzimanikatis V, Papoutsakis ET.

BMC Bioinformatics. 2007 Jun 29;8:228.PMID: 17603872 [PubMed - indexed for MEDLINE]Related articlesFree article

Inferring transcriptional regulatory networks from high-throughput data.

Wang RS, Wang Y, Zhang XS, Chen L.

Bioinformatics. 2007 Nov 15;23(22):3056-64. Epub 2007 Sep 22.PMID: 17890736 [PubMed - indexed for MEDLINE]Related articlesFree article

Motif-directed network component analysis for regulatory network inference.

Wang C, Xuan J, Chen L, Zhao P, Wang Y, Clarke R, Hoffman E.

BMC Bioinformatics. 2008;9 Suppl 1:S21.PMID: 18315853 [PubMed - indexed for MEDLINE]Related articlesFree article

An ensemble learning approach to reverse-engineering transcriptional regulatory networks from time-series gene expression data.

Ruan J, Deng Y, Perkins EJ, Zhang W.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S8.PMID: 19594885 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcriptional regulatory network refinement and quantification through kinetic modeling, gene expression microarray data and information theory.

Sayyed-Ahmad A, Tuncay K, Ortoleva PJ.

BMC Bioinformatics. 2007 Jan 23;8:20.PMID: 17244365 [PubMed - indexed for MEDLINE]Related articlesFree article

Inferring yeast cell cycle regulators and interactions using transcription factor activities.

Yang YL, Suen J, Brynildsen MP, Galbraith SJ, Liao JC.

BMC Genomics. 2005 Jun 10;6(1):90.PMID: 15949038 [PubMed - indexed for MEDLINE]Related articlesFree article

Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations.

Zare H, Sangurdekar D, Srivastava P, Kaveh M, Khodursky A.

BMC Syst Biol. 2009 Apr 14;3:39.PMID: 19366454 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data.

Kim SY, Kim Y.

BMC Bioinformatics. 2006 Jul 4;7:330.PMID: 16817975 [PubMed - indexed for MEDLINE]Related articlesFree article

Statistical methods in integrative analysis for gene regulatory modules.

Zeng L, Wu J, Xie J.

Stat Appl Genet Mol Biol. 2008;7(1):Article 28. Epub 2008 Oct 10.PMID: 18976224 [PubMed - indexed for MEDLINE]Related articlesFree article

Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data.

Wu WS, Li WH, Chen BS.

BMC Bioinformatics. 2007 Jun 8;8:188.PMID: 17559637 [PubMed - indexed for MEDLINE]Related articlesFree article

A Gibbs sampler for the identification of gene expression and network connectivity consistency.

Brynildsen MP, Tran LM, Liao JC.

Bioinformatics. 2006 Dec 15;22(24):3040-6. Epub 2006 Oct 23.PMID: 17060361 [PubMed - indexed for MEDLINE]Related articlesFree article

Inferring activity changes of transcription factors by binding association with sorted expression profiles.

Cheng C, Yan X, Sun F, Li LM.

BMC Bioinformatics. 2007 Nov 16;8:452.PMID: 18021409 [PubMed - indexed for MEDLINE]Related articlesFree article

Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae.

Vu TT, Vohradsky J.

Nucleic Acids Res. 2007;35(1):279-87. Epub 2006 Dec 14.PMID: 17170011 [PubMed - indexed for MEDLINE]Related articlesFree article

Reconstruction of genetic association networks from microarray data: a partial least squares approach.

Pihur V, Datta S, Datta S.

Bioinformatics. 2008 Feb 15;24(4):561-8. Epub 2008 Jan 18.PMID: 18204062 [PubMed - indexed for MEDLINE]Related articlesFree article

Inferring transcription factor targets from gene expression changes and predicted promoter occupancy.

Yeo ZX, Yeo HC, Yeo JK, Yeo AL, Li Y, Clarke ND.

J Comput Biol. 2009 Feb;16(2):357-68.PMID: 19193152 [PubMed - indexed for MEDLINE]Related articles

Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae.

Cokus S, Rose S, Haynor D, Grønbech-Jensen N, Pellegrini M.

BMC Bioinformatics. 2006 Aug 16;7:381.PMID: 16914048 [PubMed - indexed for MEDLINE]Related articlesFree article